4ATQ | pdb_00004atq

GABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ATP	PDB ENTRY 4ATP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		28% (W/V) PEG3350, 0.2M AMMONIUM ACETATE, 1MM PLP, 3% (V/V) DIOXANE, 10 MM GABA, 100 MM BIS-TRIS PROPANE PH 7.5, PROTEIN AT 10 MG PER ML.

Crystal Properties
Matthews coefficient	Solvent content
2.42	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.71	α = 90
b = 292.83	β = 90
c = 105.96	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC CCD		2012-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.75	97.61	100	0.12	14.3	7.4		136067		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.82	100		0.74	2.6	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4ATP	2.75	90.87	136067	7182	99.97	0.20407	0.20177	0.2	0.24803	0.24	RANDOM	35.05

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.63			-0.95		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.711
r_dihedral_angle_3_deg	14.863
r_dihedral_angle_4_deg	14.533
r_dihedral_angle_1_deg	5.608
r_angle_refined_deg	1.451
r_angle_other_deg	1.385
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_bond_other_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37887
Nucleic Acid Atoms
Solvent Atoms	546
Heterogen Atoms	264

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing